Don’t throw leftover silica DNA purification columns/buffers away! Use them up! (DIY Silica Spin Kits)

Published: June 16th, 2017   Last Modified: November 23rd, 2019

Silica based nucleic acid purification columns and kits are a common consumable in the lab. They’re used for cleaning up PCR reactions, purifying gel slices and plasmid DNA minipreps. Inevitably, when you reach the bottom of the box you are usually left with one of two scenarios: 1) You don’t have enough of a specific buffer or 2) You don’t have enough columns. Both of these scenarios usually result in the remaining components of the kit being tossed out or forgotten in your cupboard for a decade (that somehow make their way into my hands).

Why not source your own columns, mix your own buffers to both reduce waste and save money! Grab a snack, ease into your bunny slippers, this is a long one.

Continue reading “Don’t throw leftover silica DNA purification columns/buffers away! Use them up! (DIY Silica Spin Kits)”

Take a look at my gene gun! (Video at end of post)

Published: May 23rd, 2017   Last Modified: June 20th, 2018

At some point during your adventures you will find yourself having to deliver a payload of DNA/RNA into your organism of interest, usually through chemical means or by piggybacking on another organism. But what if, for whatever reason, you can’t use either method? Why not deliver your DNA coated onto gold/tungsten particles DIRECTLY INTO THE NUCLEUS at high speed through a gene gun!

Now, commercial gene guns are sold and manufactured by BioRad. However, the price tag of 10-30,000$ depending on the model is prohibitive for those who want to dip their toes into particle bombardment. How about doing it DIY style, safely, for less than 1000$ all in?

Continue reading “Take a look at my gene gun! (Video at end of post)”

CNCd Electrophoresis Gear : The Reckoning

Published: March 19th, 2017   Last Modified: June 16th, 2017

In this video I talk about how you can apply technologies like CNC routers to do your bidding, in this case to make very professional looking electrophoresis gear. I’ve included the Fusion 360 files to make your own, click the “Continue Reading” button after the embedded video.

Continue reading “CNCd Electrophoresis Gear : The Reckoning”

Just bleach it

Published: November 1st, 2016   Last Modified: September 18th, 2020

Earlier I made a post about decontaminating solutions and how to homebrew them for cheap. I had one more patent to talk about but I felt kinda burnt out (and a bit guilty that I was bullying the decontaminating solution manufacturers association (DSMA) so much ), I ended up letting it sit for a bit. But this horse isn’t quite dead yet, as I think there’s some very useful information to be gleaned by examining the solution known as DNA Zap, from Thermo.

It’s a bit of an oddity, a TWO part cleaning solution meant to destroy nucleic acids, which you apply to an area one after another. Pretty…how you say, le fancy, non? Taking a peek at the MSDS will tell you that Part A contains copper sulfate, which I hadn’t encountered in decontaminating solutions before. WHY??? WHY DO YOU NEED COPPER SULFATE??? What magic is in the mix that can possibly improve on your standard soapy/bleachy/NaOH-y goodness?

Continue reading “Just bleach it”

Where the hell have you been, pipette jockey??? The world NEEDS YOU! Upcoming stuffs

Published: September 16th, 2016   Last Modified: June 16th, 2017

Just letting you all know that I’m not dead, I haven’t been hit by a bus and I haven’t given up on science to enter the shady world of underground street fighting. I’ve been pushing hard to construct an infectious clone of a plant virus, which has been my baby for the last year and a half. I’m at the stage where I have to get the plasmid into my plants…agroinfiltration? It’s an option, but not very exciting, so instead I’ve been building various DIY particle bombardment devices!

This includes attempts at using a coilgun to shoot home made magnetite beads, an electromagnet to pull the beads INTO the leaf, and a more promising DIY gene gun that uses CO2 cartridges, and actually works!

On top of that I have articles lined up concerning DIY electrophoresis equipment, cheap digital thermometers and various useful gadgets that make our lives a bit easier. Stay tuned!

Make a Solid State Cooling Block for 50 bucks

Published: May 13th, 2016   Last Modified: May 7th, 2018

Occasionally you need to do an enzymatic reaction at temperatures lower than ambient, and some of those times you need to do it in reasonable volumes. Your thermocycler is being used by some plucky graduate student, and it wouldn’t fit anyway in those wee little cups for PCR tubes. What to do? Shell out 1000-2000$ for something commercial that you’re only going to use occasionally? NAHHHHH!!!! Whip up your own with parts bought off ebay and stuff you have lying around! 50 bucks or less, easy.

Specs? You can select a temperature and it can cool down to -2.0C in 10 minutes or less, good enough. Hindsight will appear as a theme in this write up, because I didn’t take pictures as I built the thing, so the only reasonable option was to take pictures while tearing it apart. You can pretend I’m building it by starting at the bottom. Worked well for a while, but a few critical oversights made the performance deteriorate, and there’s always time to do it right the second time.

This is a teardown of one of my prototypes. I won’t go into the wiring or the electric theory too deep, you can figure it out pretty easily by looking it up online, and half the fun is trying it yourself and screwing up, alot. Continue reading “Make a Solid State Cooling Block for 50 bucks”

Homebrew/DIY RNAlater AKA RNA Preservation Medium on the cheap!

Published: May 8th, 2016   Last Modified: June 16th, 2017

Extracting RNA from tissue is one of the most critical procedures in RNA work, considering that un-degraded RNA is the starting point for all your downstream experiments. Usually, this means taking your tissue, grinding it up in buffer and going through your standard RNA purification procedure to completion where you can breathe easy (not over the tubes!) ONLY after your RNA is safely re-suspended in RNA storage buffer, aliqouted and frozen.

Sometimes extracting RNA to completion isn’t practical, whether it’s because you’ve got 20 different samples, you’re tired and it’s 2 AM or you’re collecting samples in the middle of a jungle (Perhaps all three?). Times like these call for RNAlater Stabilization Solution, a Thermofisher product, which allows you to immerse your tissue to process later without fear of RNA degradation. Nice right? Only problem is that it costs between 800-1200$/L depending on if you buy in bulk. Turns out you can make your own for 50$/L!

Continue reading “Homebrew/DIY RNAlater AKA RNA Preservation Medium on the cheap!”

DIY Silicon dioxide DNA extraction matrix…from shoe desiccant?

Published: May 8th, 2016   Last Modified: November 17th, 2017

The grey-beards among you remember a time, when dinosaurs roamed the earth, before silicon dioxide based spin columns were commercially available. The times when you had to expose yourself to phenol/chloroform just to purify some DNA. I was trained in a similar manner, with your standard Sol’n 1-2-3 miniprep and PCI extraction. But once you have a little taste, just a taste, of the convenience, reproducibility and lack of phenol it can be hard to go back. Good spin kits (Macherey Nagel, mmm) can cost up to 2$ a prep and if you shop around you can get them for 0.50$ a prep without some of the frills, buffers or German engineering. I’ve heard of do it yourself silica matrix from various sources such as glass wool or diatomacieous earth but never really found a protocol that seemed easy and straightforward. Recently though I struck protocol gold, a method where you can make silicon dioxide DNA extraction matrix easily, cheaply and if you’re really desperate, from shoe desiccant.

Continue reading “DIY Silicon dioxide DNA extraction matrix…from shoe desiccant?”

Make your own nuclease/nucleic acid decontaminating solution

Published: May 6th, 2016   Last Modified: September 18th, 2020

There are some products from large molecular biology companies that I think are definitely worth the hefty price tag. Q5 polymerase from NEB and Superscript III from Thermofisher are two which give awesome results. The amount of R&D involved to mutate your pedestrian polymerases and give them cool and useful features must be astronomical. Not to mention paying fellow pipette jockeys to grow up huge batches, purify them to a high degree and distribute them. Worth it, take my money, hats off for making a good product.

Now, you want me to pay 35 bucks for half a liter of “ultrapure water” or for a simple buffer? There are situations where purchasing these could be called for, perhaps where traceability is absolutely necessary. For your average Joe/Jane Shmoe lab doing basic research? Naaaaaaahhhhhhh, comon buddy. One reagent I’ve come across that’s expensive to buy but costs very little to manufacture are your RNase/DNase/RNA/DNA decontaminating solutions, such as RNase away (100-400$/L) and RNaseZAP (250$/L). Why not make your own for less than 20$/L? (Up to date recipe at bottom of post)

Continue reading “Make your own nuclease/nucleic acid decontaminating solution”